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- PDB-4x9o: Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cho... -

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Basic information

Entry
Database: PDB / ID: 4x9o
TitleBeta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae soaked with octanoyl-CoA: conformational changes without clearly bound substrate
Components3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / FabH / beta-ketoacyl-acyl carrier protein synthase III
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsHou, J. / Cooper, D.R. / Shabalin, I.G. / Grabowski, M. / Shumilin, I. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
CitationJournal: to be published
Title: Structural and enzymatic studies of beta-ketoacyl-(acyl carrier protein) synthase III (FabH) from Vibrio cholerae
Authors: Hou, J. / Zheng, H. / Cooper, D.R. / Chruszcz, M. / Chordia, M.D. / Grabowski, M. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2


Theoretical massNumber of molelcules
Total (without water)78,0722
Polymers78,0722
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-29 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.705, 84.246, 134.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 3 - 350 / Label seq-ID: 3 - 350

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 / 3-oxoacyl-[acyl-carrier-protein] synthase III protein 2 / Beta-ketoacyl-ACP synthase III 2 / KAS III 2


Mass: 39036.117 Da / Num. of mol.: 2 / Mutation: C113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabH2, VC_A0751 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KLJ3, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.18M Sodium malonate pH 7.0,22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2013 / Details: Beyllium Lenses
RadiationMonochromator: Diamond 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Number: 133064 / Rmerge(I) obs: 0.094 / Χ2: 1.57 / D res high: 2.3 Å / D res low: 28 Å / Num. obs: 30415 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.222810.0452.3674.2
4.956.2210.0532.3854.4
4.324.9510.0582.9214.2
3.934.3210.0612.5964.3
3.653.9310.0742.5264.1
3.433.6510.0862.1094.5
3.263.4310.1021.8564.5
3.123.2610.1241.6644.5
33.1210.1461.4864.5
2.9310.1781.3994.5
2.812.910.211.2314.4
2.732.8110.2631.0924.4
2.652.7310.2931.1244.4
2.592.6510.3221.0524.4
2.532.5910.4051.0124.4
2.482.5310.4190.9994.3
2.432.4810.5090.9354.4
2.382.4310.5440.9044.3
2.342.3810.640.9064.4
2.32.3410.7010.8974.3
ReflectionResolution: 2.3→28 Å / Num. obs: 30415 / % possible obs: 96.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.049 / Rrim(I) all: 0.107 / Χ2: 1.565 / Net I/av σ(I): 20.955 / Net I/σ(I): 8 / Num. measured all: 133064
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.344.30.70115100.8230.3690.7960.89797.2
2.34-2.384.40.6415080.8720.3320.7240.90699.1
2.38-2.434.30.54415330.8890.2840.6170.90497.3
2.43-2.484.40.50915050.8970.2640.5760.93598
2.48-2.534.30.41915410.930.2180.4750.99998.6
2.53-2.594.40.40515010.9280.210.4581.01298.2
2.59-2.654.40.32215290.9520.1660.3641.05297.3
2.65-2.734.40.29315170.960.1520.3321.12497.9
2.73-2.814.40.26315290.9570.1360.2981.09297.5
2.81-2.94.40.2115290.9760.110.2391.23197.3
2.9-34.50.17815010.980.0920.2011.39997.3
3-3.124.50.14615180.9850.0760.1651.48697.1
3.12-3.264.50.12415220.9890.0640.141.66496.8
3.26-3.434.50.10215330.9920.0530.1161.85696.8
3.43-3.654.50.08615150.9950.0440.0972.10995.9
3.65-3.934.10.07414990.9940.040.0852.52695.4
3.93-4.324.30.06115350.9960.0330.072.59694.8
4.32-4.954.20.05814710.9950.0310.0662.92191.6
4.95-6.224.40.05315320.9960.0280.062.38594.5
6.22-284.20.04515870.9970.0240.0512.36791.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.007refinement
HKL-3000data reduction
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WZU

4wzu


Resolution: 2.3→28 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.67 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 1459 4.8 %RANDOM
Rwork0.1952 28909 --
obs0.197 28922 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.15 Å2 / Biso mean: 47.338 Å2 / Biso min: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å2-0 Å2
2---4.15 Å20 Å2
3---5.13 Å2
Refinement stepCycle: final / Resolution: 2.3→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 0 62 4558
Biso mean---40.78 -
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194569
X-RAY DIFFRACTIONr_bond_other_d0.0040.024261
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9416235
X-RAY DIFFRACTIONr_angle_other_deg0.88339686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1524.224161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05915618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025372
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021022
X-RAY DIFFRACTIONr_mcbond_it1.8872.8332560
X-RAY DIFFRACTIONr_mcbond_other1.8862.8322559
X-RAY DIFFRACTIONr_mcangle_it2.9774.233186
Refine LS restraints NCS

Ens-ID: 1 / Number: 17275 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 100 -
Rwork0.26 2127 -
all-2227 -
obs--97.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8177-0.27310.02111.535-0.69440.73340.03930.0255-0.3481-0.29460.11640.54760.1941-0.1028-0.15570.2-0.0732-0.14690.1898-0.02510.33243.434-15.75215.343
20.3905-0.0787-0.43291.5536-0.11750.96350.0030.0786-0.0045-0.27750.11490.3240.0454-0.021-0.11780.1844-0.038-0.07680.20840.01290.09565.45-2.84518.609
30.8855-0.0165-0.20592.2298-0.59910.5748-0.02570.0086-0.3277-0.37790.08460.08480.12630.0581-0.05890.1703-0.0008-0.02770.1609-0.0450.164615.231-17.72222.412
42.95870.2536-1.77172.1068-0.55791.1694-0.24670.5714-0.3772-0.41920.30941.0530.2434-0.4637-0.06270.1738-0.1435-0.26470.33880.13740.6978-4.053-12.34916.789
50.4928-0.20290.29091.4158-0.41950.6070.03860.06780.0883-0.26080.017-0.21530.06370.054-0.05560.1711-0.02560.06130.2106-0.00830.108225.7187.76917.832
60.8684-0.0249-0.02541.01750.02450.8890.04020.0490.2855-0.22470.0648-0.0025-0.143-0.0865-0.10490.177-0.0026-0.01320.15440.03920.126912.21414.66119.986
71.3286-0.03770.26351.55910.01561.3521-0.02440.00210.4781-0.16050.0681-0.1321-0.18640.1612-0.04370.1211-0.02490.04280.1119-0.00080.220520.73123.98525.58
81.0973-0.47760.5141.47880.2551.5114-0.00880.11570.5434-0.2559-0.034-0.3104-0.20910.11370.04280.1787-0.06360.05490.14110.05260.313127.25814.91819.418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 45
2X-RAY DIFFRACTION2A46 - 170
3X-RAY DIFFRACTION3A171 - 322
4X-RAY DIFFRACTION4A323 - 350
5X-RAY DIFFRACTION5B3 - 149
6X-RAY DIFFRACTION6B154 - 236
7X-RAY DIFFRACTION7B237 - 308
8X-RAY DIFFRACTION8B309 - 350

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